Technical Abstract:
We performed a comprehensive molecular genetic analysis of the Commonwealth Potato Collection (CPC), as well as material from a USDA potato collection. This analysis, one of the first to include an entire germplasm collection, has involved the deployment of six AFLP primer combinations (four PstI/MseI and two EcoRI/PstI) on more than 2000 DNA samples, and which has yielded over 400 polymorphic markers. Overall more than 150 taxa have been examined and 850,000 data points have been scored. This study has presented significant new challenges, both in terms of data capture, validation and storage, as well as to its analysis using conventional software. The data are being used in several ways: to resolve issues relating to genebank management, to resolve questions of potato taxonomy, to examine the population biology of potato taxa differing in breeding system and ploidy level, and to inform future use of potato genebanks in research and potato breeding. Our current activities include the use of ordination approaches to augment conventional phylogenetic approaches to visualize the entire dataset, as well as subsets based on taxonomic and geographical considerations. A primary goal is to use the AFLP data to flag putatively misidentified accessions or corrupted DNA samples. An ongoing analysis involves the examination of levels of AFLP diversity within and between accessions of the same species. Material has been chosen to represent the different ploidy levels as well as the different types of mating system in potato taxa. This study is revealing that variation is distributed in markedly different ways in inbreeding and outbreeding taxa, which necessitate different approaches to genebank management and sampling.